The IAF is also looking into an incident where its An-32 transport aircraft was about to land at a close runway at the Delhi airport earlier this week.
Early last week, "our radars picked up a UFO near Amritsar which was moving slowly towards the International Border with Pakistan" and a Su-30MKI was scrambled from Halwara air base to intercept it, IAF sources said here.
As the aircraft was being launched, the air traffic was asked to be cleared at heights between 25,000 and 30,000 feet as the UFO was flying at 28,000 feet, they said.
Later on, the Su-30MKI identified that the object was a weather balloon which was flying with the wind towards the border and it returned from there after being airborne for around 20 minutes, they said.
Reports suggested that two civilian planes of Thai Airways and another foreign operator were flying around 10 nautical miles away from the IAF aircraft.
The IAF denied that there was any "near-miss incident" involving its aircraft as it was under positive radar coverage and was cleared for operating in that area.
The DGCA is looking into the incident, sources said.